| Variant ID: vg0200790328 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 790328 |
| Reference Allele: T | Alternative Allele: TA,A |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 141. )
ATCATAAATTTCTCAAAACAATCAGCATCATGTAGATGAAATGGAACAATTGAAAATGCTCAATTTTGTTATTCTGTGACAGCTTGAGCTTTGTTTTTTT[T/TA,A]
AACTTAAAAGACGTTGTTTTGTCTGAATTTCAAGGTAAAGTTCAGCTACAAGTTAGAACTAGCTTGGTTTTGTATCATCCTGTTCATAGAGATTGTCAGG
CCTGACAATCTCTATGAACAGGATGATACAAAACCAAGCTAGTTCTAACTTGTAGCTGAACTTTACCTTGAAATTCAGACAAAACAACGTCTTTTAAGTT[A/TA,T]
AAAAAAACAAAGCTCAAGCTGTCACAGAATAACAAAATTGAGCATTTTCAATTGTTCCATTTCATCTACATGATGCTGATTGTTTTGAGAAATTTATGAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.90% | 18.00% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 60.80% | 39.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 81.50% | 18.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 19.40% | 80.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.90% | 24.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 17.70% | 82.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 63.30% | 35.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200790328 | T -> A | LOC_Os02g02350.2 | upstream_gene_variant ; 4652.0bp to feature; MODIFIER | N | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> A | LOC_Os02g02360.1 | downstream_gene_variant ; 1093.0bp to feature; MODIFIER | N | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> A | LOC_Os02g02380.1 | downstream_gene_variant ; 4738.0bp to feature; MODIFIER | N | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> A | LOC_Os02g02370.1 | intron_variant ; MODIFIER | N | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> TA | LOC_Os02g02350.2 | upstream_gene_variant ; 4653.0bp to feature; MODIFIER | silent_mutation | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> TA | LOC_Os02g02360.1 | downstream_gene_variant ; 1094.0bp to feature; MODIFIER | silent_mutation | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> TA | LOC_Os02g02380.1 | downstream_gene_variant ; 4737.0bp to feature; MODIFIER | silent_mutation | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |
| vg0200790328 | T -> TA | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.109; most accessible tissue: Zhenshan97 root, score: 70.636 | N | N | N | N |